Morning pace-setter Kimi Raikkonen placing best lap-time between the Mercedes duo, Hamilton made the fastest time, finishing 0.262s up on Raikkonen, a four-time winner at Spa.
Valtteri Bottas managed third fastest, four-tenths off the pace, with Red Bull’s Max Verstappen and the Championship leader Sebastian Vettel was only fifth and nearly half a second adrift of the lead Mercedes’ pace
Mercedes chief Toto Wolff suggested that the real competitive picture was not quite so clear cut.
“It’s very close,” Wolff told Sky Sports F1. “I think it’s closer than you can see. Vettel did a fantastic long run, which was much faster than everyone else.”
Red Bull speedy Daniel Ricciardo failed to get a lap with Ultra Soft rubber, following a technical problem, leaving him 1.3 seconds back in sixth position.
Near the end, thunderous rainfall soaked the vast 7-kilometer (4.3-mile) Spa circuit that cuts through the forest of Ardennes, enveloping it in darkness.
“Aquaplaning already,” Ricciardo said. “Lot of water everywhere.” Ricciardo then sought refuge back in the team garage, along with the other drivers, as the session petered out.
Renault ace Nico Hulkenberg led the chasing pack in seventh, ahead of Force India’s Esteban Ocon and Toro Rosso’s Carlos Sainz Jr., with team-mate Jolyon Palmer completed the top 10 in Belgium GP second practice.